The aim of the study is to compare the effects of Salvia hispanica (Chia) seed and Nigella sativa (Black Cumin) seed in traditionally produced dry fermented sausages with reduced nitrites on the changes in physicochemical parameters (water content, pH, and water activity), thioarbituric acid reactive substances (TBARS), color parameters, the content of nitrosopigments, and microbial counts throughout the production process. At the end of the processing, the content of biogenic amines was also determined. Five samples were analyzed during the 30-day production process: the control sample, samples with 1% and 2% additions of chia seed, and samples with 1% and 2% additions of black cumin seed. It was indicated that the addition of chia or black cumin did not exert any effect on water content or water activity changes in fermented sausages. At the end of production, the samples were characterized by low water activity, in the range of 0.798–0.813. The sausages with chia seeds were characterized by the lowest pH due to the highest proliferation of lactic acid bacteria. TBARS values did not alter in both control and black cumin sausages throughout the experiment. Microbiological analysis showed that the addition of chia or black cumin seed enhances the proliferation of the lactic acid bacteria and caused a reduction in the number of Enterobacteriaceae in comparison to the control.